If the Endless don't have souls then what is a soul? Cahciua seemed like she had emotions and thoughts, and was able to react and interact with everyone around her. Krile's parents were able to recognize Krile and enjoyed being with her and made new memories hanging out with her. Even if they "do not have souls" what does this mean?

And you can say they are being sustained by evil means, but they are not responsible for this. If you were only alive because a truly evil person was keeping you alive, does this justify killing you? The project certainly could not be continued, but whether or not it should have been shut down immediately is not black or white for me and I think it needed to be explored more.